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CHARMM: The biomolecular simulation program
An overview of the CHARMM program as it exists today is provided with an emphasis on developments since the publication of the original CHARMM article in 1983. Expand
The robustness of pollination networks to the loss of species and interactions: a quantitative approach incorporating pollinator behaviour.
Tolerance of generalized networks to species extinctions was high in the random removal scenario, with an increase in network stability if species formed new interactions, however, Anthropogenic disturbance that promote the extinction of the strongest interactors might induce a sudden collapse of pollination networks. Expand
Macrodomain-containing proteins are new mono-ADP-ribosylhydrolases
MacroD2 reversed the ARTD10-catalyzed, mono-ADP-ribosylhydrolase–mediated inhibition of glycogen synthase kinase 3β (GSK3β) in vitro and in cells, thus underlining the physiological and regulatory importance of mono- ADP- ribosylHydrolase activity. Expand
FACTS: Fast analytical continuum treatment of solvation
An efficient method for calculating the free energy of solvation of a (macro)molecule embedded in a continuum solvent is presented. It is based on the fully analytical evaluation of the volume andExpand
Predicting free energy changes using structural ensembles.
The next issue of NPG Nature Asia-Pacific will be published in May 2017, with a focus on China, Korea and South Korea. Expand
The protein folding network.
The conformation space of a 20 residue antiparallel beta-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network and provides a basis for understanding the heterogeneity of the TS and denatured state ensemble as well as the existence of multiple pathways. Expand
PARP1 ADP-ribosylates lysine residues of the core histone tails
Computational and experimental results provide strong evidence that PARP1 modifies important regulatory lysines of the core histone tails of all core histones. Expand
Prediction of aggregation rate and aggregation‐prone segments in polypeptide sequences
A model based on physicochemical properties and computational design of β‐aggregating peptide sequences is shown to be able to predict the aggregation rate over a large set of natural polypeptide sequences. Expand
Epigenetic mechanisms regulate stage differentiation in the minimized protozoan Giardia lamblia
The results provide the first direct evidence for epigenetic regulation of gene expression in this simple eukaryote, suggesting that regulation of histone acetylation is involved in the control ofGiardia stage differentiation, and identifies epigenetic mechanisms as a promising target to prevent Giardia transmission. Expand
Thermodynamics and Kinetics of Folding of Two Model Peptides Investigated by Molecular Dynamics Simulations
The folding of an R-helix and a ‚-hairpin was studied by 862 molecular dynamics simulations with an implicit solvation model that allowed sampling of a total of 4 Is. The average effective energy isExpand